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Scherf M, Koy C, Röwer C, Neamtu A, Glocker MO. Characterization of Phosphorylation-Dependent Antibody Binding to Cancer-Mutated Linkers of C 2H 2 Zinc Finger Proteins by Intact Transition Epitope Mapping-Thermodynamic Weak-Force Order Analysis. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:171-181. [PMID: 36656134 DOI: 10.1021/jasms.2c00244] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
With Intact Transition Epitope Mapping-Thermodynamic Weak-force Order (ITEM-TWO) analysis in combination with molecular modeling, the phosphorylation-dependent molecular recognition motif of the anti-HpTGEKP antibody has been investigated with binary and ternary component mixtures consisting of antibody and (phospho-) peptides. Amino acid sequences have been selected to match either the antibody's recognition motif or the cancer-related zinc finger protein mutations and phosphorylations of the respective amino acid residues. Upon electrospraying of all the components of the mixtures, that is, hexapeptides, antibody, and intact immune complexes, the produced ions were subjected to mass spectrometric mass filtering. The antibody ions as well as the immune complex ions traversed into the mass spectrometer's collision chamber, whereas paths of unbound peptide ions were blocked prior to entering the collision cell. After dissociation of the multiply charged immune complexes in the gas phase, the complex-released peptide ions were recorded after having traversed the second mass filter. Complex-released peptides were unambiguously identified by their masses using mass analysis with isotope resolution. From the results of our studies with seven (phospho-) peptides with distinct amino acid sequences, which resembled either the antibody's binding motif or mutations, we conclude the following: (i) A negatively charged phospho group, located near the peptide's N-terminus is mandatory for antibody binding when placed on the peptide surface at a precise distance to the C-terminally located positively charged ε-amino group of a lysinyl residue. (ii) A bulky amino acid residue, such as the tyrosinyl residue at the N-terminal position of the (phospho-) threoninyl residue, abolishes antibody binding. (iii) Two closely spaced phospho groups negatively interfere with the surface polarity pattern and abolish antibody binding as well. (iv) Non-phosphorylated peptides are not binding partners of the anti-HpTGEKP antibody.
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Affiliation(s)
- Maximilian Scherf
- Proteome Center Rostock, University Medicine Rostock and University of Rostock, Schillingallee 69, 18059 Rostock, Germany
| | - Cornelia Koy
- Proteome Center Rostock, University Medicine Rostock and University of Rostock, Schillingallee 69, 18059 Rostock, Germany
| | - Claudia Röwer
- Proteome Center Rostock, University Medicine Rostock and University of Rostock, Schillingallee 69, 18059 Rostock, Germany
| | - Andrei Neamtu
- TRANSCEND Centre, Regional Institute of Oncology (IRO) Iasi, Str. General Henri Mathias Berthelot Nr. 2-4, 700483 Iasi, Romania
- Department of Physiology, Grigore T. Popa University of Medicine and Pharmacy of Iasi, Str. Universitatii Nr. 16, 700115 Iasi, Romania
| | - Michael O Glocker
- Proteome Center Rostock, University Medicine Rostock and University of Rostock, Schillingallee 69, 18059 Rostock, Germany
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Zhang Y, He F, Zhang Y, Dai Q, Li Q, Nan J, Miao R, Cheng B. Exploration of the regulatory relationship between KRAB-Zfp clusters and their target transposable elements via a gene editing strategy at the cluster specific linker-associated sequences by CRISPR-Cas9. Mob DNA 2022; 13:25. [PMID: 36357895 PMCID: PMC9647903 DOI: 10.1186/s13100-022-00279-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 09/29/2022] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Krüppel Associated Box-containing Zinc Finger Proteins (KRAB-ZFPs), representing the largest superfamily of transcription factors in mammals, are predicted to primarily target and repress transposable elements (TEs). It is challenging to dissect the distinct functions of these transcription regulators due to their sequence similarity and diversity, and also the complicated repetitiveness of their targeting TE sequences. RESULTS Mouse KRAB-Zfps are mainly organized into clusters genomewide. In this study, we revealed that the intra-cluster members had a close evolutionary relationship, and a similar preference for zinc finger (ZnF) usage. KRAB-Zfps were expressed in a cell type- or tissue type specific manner and they tended to be actively transcribed together with other cluster members. Further sequence analyses pointed out the linker sequences in between ZnFs were conserved, and meanwhile had distinct cluster specificity. Based on these unique characteristics of KRAB-Zfp clusters, sgRNAs were designed to edit cluster-specific linkers to abolish the functions of the targeted cluster(s). Using mouse embryonic stem cells (mESC) as a model, we screened and obtained a series of sgRNAs targeting various highly expressed KRAB-Zfp clusters. The effectiveness of sgRNAs were verified in a reporter assay exclusively developed for multi-target sgRNAs and further confirmed by PCR-based analyses. Using mESC cell lines inducibly expressing Cas9 and these sgRNAs, we found that editing different KRAB-Zfp clusters resulted in the transcriptional changes of distinct categories of TEs. CONCLUSIONS Collectively, the intrinsic sequence correlations of intra-cluster KRAB-Zfp members discovered in this study suggest that the conserved cluster specific linkers played crucial roles in diversifying the tandem ZnF array and the related target specificity of KRAB-Zfps during clusters' evolution. On this basis, an effective CRISPR-Cas9 based approach against the linker sequences is developed and verified for rapidly editing KRAB-Zfp clusters to identify the regulatory correlation between the cluster members and their potential TE targets.
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Affiliation(s)
- Yang Zhang
- School of Life Sciences, Lanzhou University, Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, Lanzhou, Gansu, People's Republic of China, 730000
| | - Fei He
- School of Life Sciences, Lanzhou University, Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, Lanzhou, Gansu, People's Republic of China, 730000
| | - Yanning Zhang
- School of Life Sciences, Lanzhou University, Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, Lanzhou, Gansu, People's Republic of China, 730000
| | - Qian Dai
- Departments of Obstetrics & Gynecology and Pediatrics, West China Second University Hospital, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Development and Related Diseases of Women and Children Key Laboratory of Sichuan Province, Sichuan University, Chengdu, Sichuan, People's Republic of China, 610041
| | - Qintong Li
- Departments of Obstetrics & Gynecology and Pediatrics, West China Second University Hospital, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Development and Related Diseases of Women and Children Key Laboratory of Sichuan Province, Sichuan University, Chengdu, Sichuan, People's Republic of China, 610041
| | - Jing Nan
- School of Life Sciences, Lanzhou University, Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, Lanzhou, Gansu, People's Republic of China, 730000
| | - Ruidong Miao
- School of Life Sciences, Lanzhou University, Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, Lanzhou, Gansu, People's Republic of China, 730000
| | - Bo Cheng
- School of Life Sciences, Lanzhou University, Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, Lanzhou, Gansu, People's Republic of China, 730000.
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Bao L, Wang M, Fan Q. Hsa_circ_NOTCH3 regulates ZNF146 through sponge adsorption of miR-875-5p to promote tumorigenesis of hepatocellular carcinoma. J Gastrointest Oncol 2021; 12:2388-2402. [PMID: 34790400 DOI: 10.21037/jgo-21-567] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 10/19/2021] [Indexed: 12/12/2022] Open
Abstract
Background To explore the specific mechanism of circular RNA (circRNA) in the occurrence and development of hepatocellular carcinoma (HCC), and provide new ideas for its diagnosis and treatment. Methods Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) was for evaluating the expression of circ_NOTCH3 in liver cancer tissues and matched normal tissues and related cell lines. After overexpression or co-expression of circ_NOTCH3 or microRNA (miRNA) in cells, the changes in cell function were analyzed. Bioinformatics analysis and dual luciferase report analysis were utilized to predict and verify the binding site between circ_NOTCH3 and miRNA. Western blotting was applied to detect gene expression alterations. Additionally, in vivo tumor growth was also utilized to further assess the influence of knocking-down circ_NOTCH3 on the progression of HCC. Results It was confirmed circ_NOTCH3 was highly expressed in HCC specimens and cells. The proliferation, migration, invasion, and oxaliplatin-resistance potential of HCC could be restrained by silencing circ_NOTCH3 or by ectopic expression of miR-875-5p in vitro. In terms of mechanism, circ_NOTCH3 directly binds to miR-875-5p, regulating its activity by targeting the 3'-UTR of ZNF146. Overexpression of circ_NOTCH3 evidently overturned the diminishing influence of miR-875-5p mimics on HCC cells. Conclusions As an oncogene, circ_NOTCH3 can trigger the proliferation, invasion, migration, and oxaliplatin resistance of HCC cells through the miR-875-5p/ZNF146 axis, and may be a promising target for the treatment of HCC.
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Affiliation(s)
- Lei Bao
- Department of Pathology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, China
| | - Min Wang
- Department of Pathology, Qishan (Infectious Disease) Hospital of Yantai, Yantai, China
| | - Qiqi Fan
- Department of Liver Disease, Qingdao No. 6 People's Hospital, Qingdao, China
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